[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Apr 18 15:25:55 CEST 2019

I second the idea of reproducing with the Windows build commands, which have to do more than 'just' build for a particular architecture. One might test the hypothesis that it is staged install that is causing the problem with 

  StagedInstalll: no

in the DESCRIPTION file.

Makevars is evaluated on Windows, unless there's a Makevars.win. cleanup is not, but cleanup.win is.


On 4/18/19, 8:38 AM, "Bioc-devel on behalf of Mike Smith" <bioc-devel-bounces using r-project.org on behalf of grimbough using gmail.com> wrote:

    I can reproduce the error using R-3.6.0beta and running the following two
    steps to replicate the Bioc builder commands:
    R CMD build --keep-empty-dirs --no-resave-data Rdisop
    rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir &&
    C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch
    --build --library=Rdisop.buildbin-libdir Rdisop_1.43.4.tar.gz
    Bit of a guess, and I don't know why this would have changed, but
    the Rdisop_1.43.4.tar.gz produced by step one contains the *.o files
    referenced in the error.  If these were produced for 64-bit architecture
    then they'll fail when the build process tries to use them for the 32-bit
    binary.  Perhaps your Rcpp edits removed some cleanup code that was there
    before?  I note there's no Makevars.win or cleanup.win but my memory is a
    bit fuzzy on whether only versions with *.win will be run on Windows or if
    that's just a way to provide alternative code if needed.
    On Thu, 18 Apr 2019 at 11:35, Neumann, Steffen <sneumann using ipb-halle.de>
    > Hi,
    > with the next release coming up, I am out of wits regarding the failure at
    > http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html
    > which exists since before April this year, when we committed
    > some changes to get rid of the RcppClassic dependency.
    > Max Helf succeeded to build locally on windows without problem.
    > So it seems that Rdisop has issues with the BioC windows build
    > environment, but I totally fail to see the reason.
    > Could it be the new staged installation ?
    > But I wouldn't know why that'd affect the compile/linking.
    > The issue is tracked at
    > https://github.com/sneumann/Rdisop/issues/13
    > Any help/pointers appreciated.
    > Yours,
    > Steffen
    > --
    > IPB Halle                    AG Massenspektrometrie & Bioinformatik
    > Dr. Steffen Neumann          http://www.IPB-Halle.DE
    > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
    > 06120 Halle                       +49 (0) 345 5582 - 0
    > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
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